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ensembl-gh-mirror
ensembl
Commits
40663f1e
Commit
40663f1e
authored
12 years ago
by
Andy Yates
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More warnings when we fail to load DBs & the VERBOSE flag is on
parent
ce96cdd8
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1 changed file
modules/Bio/EnsEMBL/Registry.pm
+17
-1
17 additions, 1 deletion
modules/Bio/EnsEMBL/Registry.pm
with
17 additions
and
1 deletion
modules/Bio/EnsEMBL/Registry.pm
+
17
−
1
View file @
40663f1e
...
...
@@ -1656,6 +1656,7 @@ sub load_registry_from_db {
}
# Register Core like databases
my
$core_like_dbs_found
=
0
;
foreach
my
$type
(
qw(core cdna vega vega_update otherfeatures rnaseq)
)
{
my
@dbs
=
grep
{
/^
[
a
-
z
]
+
_
[
a
-
z0
-
9
]
+
(?:
_
[
a
-
z0
-
9
]
+
)?
# species name
...
...
@@ -1667,6 +1668,10 @@ sub load_registry_from_db {
_
/
x
}
@dbnames
;
if
(
@dbs
)
{
$core_like_dbs_found
=
1
;
}
foreach
my
$database
(
@dbs
)
{
if
(
index
(
$database
,
'
collection
'
)
!=
-
1
)
{
# Skip multi-species databases.
...
...
@@ -1685,7 +1690,7 @@ sub load_registry_from_db {
/
x
);
if
(
!
defined
(
$species
)){
warn
"
for
$database
cannot get species??
\n
";
warn
"
Cannot extract species name from database '
$database
'
";
}
my
$dba
=
...
...
@@ -1745,6 +1750,9 @@ sub load_registry_from_db {
}
}
## end foreach my $multidb (@multi_dbs)
if
(
!
$core_like_dbs_found
&&
$verbose
)
{
print
("
No core-like databases found. Check your DB_VERSION (used '
$software_version
')
\n
");
}
# User upload DBs
...
...
@@ -1825,6 +1833,10 @@ sub load_registry_from_db {
my
@variation_dbs
=
grep
{
/^[a-z]+_[a-z0-9]+(?:_[a-z0-9]+)?_variation_(?:\d+_)?\d+_/
}
@dbnames
;
if
(
!
@variation_dbs
&&
$verbose
)
{
print
("
No variation databases found
\n
");
}
for
my
$variation_db
(
@variation_dbs
)
{
if
(
index
(
$variation_db
,
'
collection
'
)
!=
-
1
)
{
...
...
@@ -1901,6 +1913,10 @@ sub load_registry_from_db {
}
else
{
my
@funcgen_dbs
=
grep
{
/^[a-z]+_[a-z0-9]+(?:_[a-z0-9]+)?_funcgen_(?:\d+_)?\d+_/
}
@dbnames
;
if
(
!
@funcgen_dbs
&&
$verbose
)
{
print
("
No funcgen databases found
\n
");
}
for
my
$funcgen_db
(
@funcgen_dbs
)
{
if
(
index
(
$funcgen_db
,
'
collection
'
)
!=
-
1
)
{
...
...
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